2MRP

NMR solution structure of the Ubiquitin like domain (UBL) of DNA-damage-inducible 1 protein (Ddi1)

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1 mM [U-100% 15N] Ddi1UBL, 5 % [U-99% 2H] D2O, 95 % H2O, 20 mM sodium phosphate, 3 mM TCEP	95% H2O/5% D2O	10	6.8	ambient atm	295.5
2	2D 1H-1H TOCSY	1 mM [U-100% 15N] Ddi1UBL, 5 % [U-99% 2H] D2O, 95 % H2O, 20 mM sodium phosphate, 3 mM TCEP	95% H2O/5% D2O	10	6.8	ambient atm	295.5
3	2D 1H-1H NOESY	1 mM [U-100% 15N] Ddi1UBL, 5 % [U-99% 2H] D2O, 95 % H2O, 20 mM sodium phosphate, 3 mM TCEP	95% H2O/5% D2O	10	6.8	ambient atm	295.5
4	3D H(CCO)NH	1 mM [U-100% 15N] Ddi1UBL, 5 % [U-99% 2H] D2O, 95 % H2O, 20 mM sodium phosphate, 3 mM TCEP	95% H2O/5% D2O	10	6.8	ambient atm	295.5
5	3D 1H-13C NOESY	1 mM [U-100% 15N] Ddi1UBL, 5 % [U-99% 2H] D2O, 95 % H2O, 20 mM sodium phosphate, 3 mM TCEP	95% H2O/5% D2O	10	6.8	ambient atm	295.5
6	3D HNCO	1 mM [U-100% 13C; U-100% 15N] Ddi1UBL, 5 % [U-99% 2H] D2O, 95 % H2O, 20 mM sodium phosphate, 3 mM TCEP	95% H2O/5% D2O	10	6.8	ambient atm	295.5
7	3D HN(CA)CO	1 mM [U-100% 13C; U-100% 15N] Ddi1UBL, 5 % [U-99% 2H] D2O, 95 % H2O, 20 mM sodium phosphate, 3 mM TCEP	95% H2O/5% D2O	10	6.8	ambient atm	295.5
8	3D HN(CO)CA	1 mM [U-100% 13C; U-100% 15N] Ddi1UBL, 5 % [U-99% 2H] D2O, 95 % H2O, 20 mM sodium phosphate, 3 mM TCEP	95% H2O/5% D2O	10	6.8	ambient atm	295.5
9	3D HNCA	1 mM [U-100% 13C; U-100% 15N] Ddi1UBL, 5 % [U-99% 2H] D2O, 95 % H2O, 20 mM sodium phosphate, 3 mM TCEP	95% H2O/5% D2O	10	6.8	ambient atm	295.5
10	3D CBCA(CO)NH	1 mM [U-100% 13C; U-100% 15N] Ddi1UBL, 5 % [U-99% 2H] D2O, 95 % H2O, 20 mM sodium phosphate, 3 mM TCEP	95% H2O/5% D2O	10	6.8	ambient atm	295.5
11	3D HNCACB	1 mM [U-100% 13C; U-100% 15N] Ddi1UBL, 5 % [U-99% 2H] D2O, 95 % H2O, 20 mM sodium phosphate, 3 mM TCEP	95% H2O/5% D2O	10	6.8	ambient atm	295.5
12	3D C(CO)NH	1 mM [U-100% 13C; U-100% 15N] Ddi1UBL, 5 % [U-99% 2H] D2O, 95 % H2O, 20 mM sodium phosphate, 3 mM TCEP	95% H2O/5% D2O	10	6.8	ambient atm	295.5
13	RDC	1 mM [U-100% 15N] Ddi1UBL, 5 % [U-99% 2H] D2O, 45 % H2O, 10 mM sodium phosphate, 3 mM TCEP, 5 % C12E5, 45 % n-hexanol	95% H2O/5% D2O	10	6.8	ambient atm	295.5
14	RDC	1 mM [U-100% 15N] Ddi1UBL, 5 % [U-99% 2H] D2O, 45 % H2O, 10 mM sodium phosphate, 3 mM TCEP, 5 % C12E5, 45 % n-hexanol	95% H2O/5% D2O	10	6.8	ambient atm	315

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600

NMR Refinement
Method	Details	Software
simulated annealing		CARA

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	10
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	peak picking	CARA	1.8.1	Keller and Wuthrich
2	chemical shift assignment	CARA	1.8.1	Keller and Wuthrich
3	collection	TopSpin	2.1	Bruker Biospin
4	processing	TopSpin	2.1	Bruker Biospin
5	data analysis	TopSpin	2.1	Bruker Biospin
6	structure solution	ARIA	2.1	Linge, O'Donoghue and Nilges
7	refinement	ARIA	2.1	Linge, O'Donoghue and Nilges
8	backbone torsion angles prediction	TALOS	TALOS+	Cornilescu, Delaglio and Bax

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.